Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_086508166.1 BZY95_RS01120 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_002151265.1:WP_086508166.1 Length = 371 Score = 188 bits (477), Expect = 2e-52 Identities = 118/340 (34%), Positives = 178/340 (52%), Gaps = 12/340 (3%) Query: 21 DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKRNVAMVYQ 80 DL +E G V +GP+ GK++L+R++AGL+ + G + DG + +P Q+R++ MV+Q Sbjct: 23 DLTIEDGEFVVFVGPSGCGKSTLLRMIAGLEDISHGEMRLDGERINEVPPQERDIGMVFQ 82 Query: 81 QFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQQQRT 140 + YP +TV N+A ++++ D A I R V AAE+L L L+R P LSGGQ+QR Sbjct: 83 SYALYPHMTVAENMAFGLKLARTDKAEIRRRVEHAAEMLHLGELLERKPKELSGGQRQRV 142 Query: 141 ALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEALLLGG 200 A+ R LVK ++ L DEPL+NLD LR ++R ++ ++ + GA +Y T + EA+ L Sbjct: 143 AIGRTLVKEPAVFLFDEPLSNLDAALRVDMRVQIAELHRRLGATMIYVTHDQVEAMTLAD 202 Query: 201 NTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLDVTKSGNVFTRPSGVTIPVP 260 L GR+ Q G + +Y P L A P +N + V R S V +P Sbjct: 203 RIVLLAGGRIAQVGAPLSLYHFPATLEVARFIGSPRINVIPVEVLDPGRQRTS-VRLPDG 261 Query: 261 SHLAVVPDG-------PVTIAFHPHHLGLAPQTGDAARLQARTLVSEITGSESFVHLEYD 313 + LAV DG T+A + P D ARL AR +V+E G E+ HL + Sbjct: 262 ATLAVAVDGARLRAGDKATLAVRAEDF-VTPADAD-ARLTARLMVAERLGYETLAHLRVE 319 Query: 314 GVRWVMLAH--GIHDIDPDMEVEAFLDTRHLMAFGSDGRA 351 GV + G+ ++ VE L F +DG+A Sbjct: 320 GVSETLTQRLDGLTRLEDGQAVELGLSGERCHLFAADGKA 359 Lambda K H 0.319 0.136 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 329 Number of extensions: 17 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 371 Length adjustment: 29 Effective length of query: 329 Effective length of database: 342 Effective search space: 112518 Effective search space used: 112518 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory